A phototrophic gammaproteobacterium designated strain JA395T was isolated from a sediment sample collected from the coast of Birds' Island in the southern sector of Chilika Lagoon, India. The bacterium is a Gram-negative, motile coccus with a single polar flagellum. Bacteriochlorophyll a, and lycopene as major carotenoid. C16:0, C16:1ω7c/C16:1ω6c and C18:1ω7c are the major cellular fatty acids of strain JA395T. The 16S rRNA gene sequence of strain JA395T clusters with those of species of the genus Thiorhodococcus belonging to the class Gammaproteobacteria. The highest sequence similarities of strain JA395T were found with the type strains of Thiorhodococcus minor (96.8%), Thiorhodococcus mannitoliphagus (96.3%), Thiorhodococcus bheemlicus (95.8%), “Thiorhodococcus drewsii” (95.4%),and Thiorhodococcus kakinadensis (95.0%). The genomic DNA base composition of strain JA395T (=KCTC 5710T=NBRC 104958T) was 57.8 mol% G + C (by HPLC). Based on the 16S rRNA gene sequence analysis, morphological and physiological characteristics, strain JA395T is sufficiently different from other Thiorhodococcus species and we describe this as a new species, Thiorhodococcus modestalkaliphilus sp. nov.

Fluorescent in situ hybridization (FISH) and confocal scanning laser microscopy (CSLM) are the key techniques used to investigate bacterial community structure at wastewater treatment plants. An optimum nitrifying bacterial population is necessary for nitrification, which plays a significant ecological role in regulating the overall quality of water. Nitrifying bacteria mainly appear as dense aggregates within activated sludge flocs. The impacts of five different pre-treatment methods (physical, chemical, enzymatic and combinations) on floc dispersion from two different wastewater treatment plants were determined. The effect of pre-treatment on the enumeration of the nitrifying bacterial population was also investigated. This study on floc dispersion using CSLM images showed sonication was the superior method for all the samples tested, irrespective of the sludge type. For samples from industrial wastewater plants, an optimized sonication level of 8 W for 8 min could reduce the floc size to 10 μm, whereas for domestic wastewater samples, the floc size was reduced to 10 μm at 8 W for 5 min. The maximum number of nitrifying bacterial cells was observed at this optimized level for different samples. A decrease in the number of cells was observed beyond this optimized level for both the plants. The results presented here highlight the importance of optimizing pre-treatment methods for different types of wastewater for accurate bacterial community analysis using FISH-CSLM.

We investigated the survival mechanisms of freeze-dried or liquid-dried (L-dried) yeast cells in ampoules. Type strains of various yeasts were freeze-dried or L-dried and sealed in ampoules under high vacuum (< 1 Pa) or low vacuum (4.8 × 104 Pa), then stored at 37ºC (accelerated storage test) for up to 17 weeks. Among strains in each of the genera Saccharomyces, Saccharomycopsis, Debaryomyces, and Pichia, survival rates immediately after freeze-drying varied more widely than those after L-drying. Freeze-dried cells stored at 4.8 × 104 Pa had lower survival rates than those stored at < 1 Pa. L-dried cells stored at 4.8 × 104 Pa also had lower survival rates than those stored at < 1 Pa, but the decrease in survival was not as marked as in freeze-dried cells. Strains that had high survival rates immediately after freeze-drying tended to have small cells, to be osmotolerant, and to be able to utilize many kinds of carbohydrates. L-dried cells of most Candida strains had stable survival rates regardless of the vacuum pressure. In basidiomycetous yeasts, strains forming extracellular polysaccharides had markedly lower survival.

To gain knowledge about the significance of phosphoenolpyruvate (PEP) carboxykinase (PCK) in Streptococcus bovis, the sequence of the gene encoding PCK (pck) was determined. Transcriptional analysis indicated that the pck is transcribed in a monocistronic fashion. The level of pck-mRNA was higher when cells were grown on lactose than on glucose, suggesting that PCK synthesis increases when the growth rate is low. The pck-mRNA level was higher in a mutant lacking ccpA, which encodes the catabolite control protein A (CcpA), than in the parent strain, suggesting that pck transcription is suppressed by CcpA. S. bovis PCK showed oxaloacetate (OAA)-decarboxylating activity, but no PEP-carboxylating activity (reverse reaction). In S. bovis, OAA was speculated to be produced from PEP via pyruvate. Disruption of pck in S. bovis resulted in decreased growth rate and cell yield. When a pck-disrupted mutant was grown in a medium lacking amino acids, the lag phase was longer and the cell yield was lower than the case of the parent strain. These results suggest that pck is involved in the initiation of growth, including the induction of amino acid synthesis and energy metabolism.

Molecular analyses of 16S ribosomal RNA genes (rDNA) revealed that microbial communities in the rhizosphere are highly complex. To systematically characterize the cell size of the bacteria in the rhizosphere, we selected bacteria that potentially could be passed through 0.22- or 0.45-μm-pore-size filters and then PCR amplified the 16S rDNA genes using the universal primer pairs 27F/1492R and 63F/1387R. The PCR-amplified rDNAs extracted from bacteria that had been passed through 0.45-μm-pore-size filters could be detected in agarose gels after electrophoresis; whereas after filtration of the bacteria through 0.22-μm-pore-size filters no PCR-amplified rDNAs were found. Comparison of random cloning and sequencing of the libraries of the PCR-amplified rDNAs with or without cell size selection showed that bacteria belonging to the candidate phylogenic divisions of OD1 (OP11-derived 1), OP11, TM7, and OP5 can be concentrated by cell size selection using 0.45-μm-pore-size filters, but not by using 0.22-μm-pore-size filters. OD1, OP11, TM7 and OP5 bacteria have yet to be cultivated; therefore, our concentration method may be used as an initial step in studies to analyze the structural properties of OD1, OP11, and TM7 bacteria.

As far as known, sporulation modes in prokaryotes include formation of endospores exemplified by Firmicutes bacteria, myxospores by myxobacteria and arthrospores by actinomycetes. Here we describe Thermosporothrix hazakensis strain SK20-1T belonging to the phylum Chloroflexi with a life cycle including a novel prokaryotic sporulation mode. Microscopic observations showed that strain SK20-1T formed multiple exospores per mother cell by budding in branched aerial mycelia. Although branched aerial mycelia are characteristic of actinomycetes, multiple budding sporulation has not been previously described in prokaryotes. The strain SK20-1T could be a model microbe for cellular differentiation with multiple budding spore formation.

Strain LXD30T was isolated from rhizosphere soil of a plant of the species Camptotheca acuminata Decne which is native to warm, humid stream banks in southern China. Analysis of the 16S rRNA gene sequence revealed that the Gram-negative, rod-shaped bacterium fell within the realm of the genus Rhizobium and was most closely related to Rhizobium huautlense SO2T (96.4% sequence similarity) and Rhizobium cellulosilyticum LMG 23642T (96.4%). The isolate grew optimally at pH7.0 and 25-28ºC in the presence of 0-1% (w/v) NaCl. Major fatty acids were C16:0 (17.5%) and summed feature 7 (C18:1ω7c/ω9t/ω12t, 58.3%). Unequivocally low 16S rRNA (<97%), recA (<92%) and atpD (<90%) gene sequence similarities to all existing species of the genus and phenotypic characteristics all suggested that strain LXD30T (=KCTC 22609T=CGMCC 1.8903T) represents a novel Rhizobium species, for which the name Rhizobium kunmingense sp. nov. is proposed.

A finished compost sample was examined for bacteriocin-like substance production against five pathogenic bacteria: Salmonella typhimurium EF 85-9, Escherichia coli O157:H7 ATCC 43888, Enterococcus faecalis JCM 8726, Staphylococcus aureus JCM 2151, and Yersinia enterocolitica JCM 7577. At the preliminary detection of bacterial strains exhibiting antimicrobial activity from the compost sample, thirteen strains could be isolated. Screening of the inhibitory activity was done using agar-well diffusion assay and Microtiter plate growth assay. Six bacterial strains from the compost showed an antimicrobial activity against one or more of the tested indicator strains. Four strains (M1-M4) belonged to Shigella species and the other two strains (M5 and M6) belonged to Salmonella species. The antimicrobial activity was sensitive for α-chymotrypsin and papain. The antimicrobial substances from M3, M4 and M6 were heat stable when heated for 15 min at 121°C with 100% relative activity. The bacteriocin-like substance produced by strain M2 was partially characterized. It exhibited an inhibitory activity against the tested food-borne pathogenic and spoilage bacteria, except Enterobacter aerogenes JCM 1235 and Lactobacillus plantarum subsp. plantarum JCM 1149. It was stable at a wide range of pH (3-11). There was no loss of activity for up to 3 weeks when stored at 4 and −20ºC or for up to 2 weeks when stored at 28 and −80ºC. This is the first report indicating the presence of bacteriocin-like activity in animal manure compost.